The Boo you mentioned, or rather, the item that transformed Mario into a Boo in some games, would actually be a good idea - but more as an item than an assist trophy.

Captain N: The game Master: Using the pause button on his belt, freezing everybody on the screen for a couple seconds, except the one who called him.

Shantae: Either using her hair as a whip like in Pirate's curse, or one of her transformations.

Alex Kidd: Forces everyone (including the one who activated the Trophy) into a game of Jenken (Rock-Paper-Scissors). Whoever looses to Alex Kidd gets a Megaton punch from him, potentially costing a life.

Kammy Koopa: Blasting your ennemies with some spells for some time.

Baby Mario: Is in his bubble and crying annoyingly loudly, just like when you lost him in SMW2: Yoshi's Island. Everybody looses health or racks up some damage as long as he's crying.

And we already got a Steve in the game anyway

Lol this 

I would like to see some Startropics representation, either in the form of Mike Jones being playable or being an assist. If he's the latter then he could easily toss baseballs at all but the summoner.

That's a cool idea too!

I think Nintendo should scour forums like this, looking for fans' ideas!

Now I want an Airship level:

Cannons, Bullet Bills and Flamethrowers everywhere, those screw platforms on the sides, Monty moles popping out of the ground, throwing their wrenches, you name it.

And now I wish I could build a stage in SMM2 and import it into SSBU.

Other Assist trophies:

Dr. Robotnik (yes, I know, he's called Eggman now, but at the time, he still was Robotnik) comes with his ship with the Wrecking ball, just like at the end of green hill zone on Sonic the Hedgehog. Whoever gets hit by the wrecking ball is in a world of hurt, but the ball is pretty slow and thus easy to avoid.

Some of the minibosses from the subspace emissary from SSBB

Builder Mario, remodeling the stage around you with new blocks, platforms, and so on. also removing existing ones. Basically, the stage builder on AI over an existing stage.

A variety of Zelda Bosses should appear and interact with the environment, including destroying it too XD.
Also,
Bub and Bob from Bubble Bobble. They could run around the stage capturing people in bubbles leaving them open for other players to attack them, popping them in a bubble will cause more damage than regular attacks too.

I personally think Bub and Bob, Bomberman, Crash Bandicoot, Spiro, Tails and Dr Robotnik (and maybe Knuckles) should be playable characters, if not then they should at least be assist trophies (I know bomberman is already an assist trophy). Some of these characters may not have a lot of attacks in their native games but if Pacman & Mr Game & Watch can make a good playable characters, then these should be able to too.

Bubble Bobble would be great. Alternatively, they make special bubbles, like the thunder or flame bubbles, and when somebody strikes those, all bubbles of that element burst, raining damage on his enemies.